genomic selection and systems biology – lessons from dairy cattle breeding
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Genomic selection and systems biology – lessons from dairy cattle breeding. Dairy Cattle. 9 million cows in US Attempt to have a calf born every year Replaced after 2 or 3 years of milking Bred via AI Bull semen collected several times/week. Diluted and frozen - PowerPoint PPT PresentationTRANSCRIPT
J. B. ColeAnimal Improvement Programs LaboratoryAgricultural Research Service, USDABeltsville, MD 20705-2350, USA
2013
Genomic selection and systems biology – lessons from dairy cattle breeding
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (2) Cole
Dairy Cattle
9 million cows in US Attempt to have a calf born every year Replaced after 2 or 3 years of milking Bred via AI Bull semen collected several times/week.
Diluted and frozen Popular bulls have 10,000+ progeny Cows can have many progeny though super
ovulation and embryo transfer
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (3) Cole
Data Collection
Monthly recording Milk yields Fat and Protein percentages Somatic Cell Count (Mastitis indicator)
Visual appraisal for type traits Breed Associations record pedigree
Calving difficulty and Stillbirth
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (4) Cole
Traditional evaluations 3X/year Yield
Milk, Fat, Protein Type
Stature, Udder characteristics, feet and legs
Calving Calving Ease, Stillbirth
Functional Somatic Cell, Productive Life, Fertility
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (5) Cole
Use of evaluations Bulls to sell semen from Parents of next generation of bulls Cows for embryo donation
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (6) Cole
Parents Selected
Dam Inseminated
Embryo Transferred to Recipient Bull Born
Semen collected (1yr)Daughters Born (9 m later)
Daughters have calves (2yr later)Bull Receives Progeny Test (5 yrs)
Lifecycle of bull
Genomic Test
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (7) Cole
Benefit of genomics
Determine value of bull at birth Increase accuracy of selection Reduce generation interval Increase selection intensity Increase rate of genetic gain
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (8) Cole
History of genomic evaluations
Dec. 2007 BovineSNP50 BeadChip available Apr. 2008 First unofficial evaluation
released Jan. 2009 Genomic evaluations official for
Holstein and Jersey Aug. 2009 Official for Brown Swiss Sept. 2010 Unofficial evaluations from 3K
chipreleased
Dec. 2010 3K genomic evaluations to be official
Sept. 2011 Infinium BovineLD BeadChip available
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (9) Cole
Cattle SNP Collaboration - iBMAC
Develop 60,000 Bead Illumina iSelect® assay
USDA-ARS Beltsville Agricultural Research Center: Bovine Functional Genomics Laboratory and Animal Improvement Programs Laboratory
University of Missouri
University of Alberta USDA-ARS US Meat
Animal Research Center
Started w/ 60,800 beads – 54,000 useable SNP
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (10) Cole
Participants
Illumina Marylinn Munson Cindy Lawley Christian Haudenschild
BARC Curt Van Tassell Lakshmi Matukumalli Tad Sonstegard
Missouri Jerry Taylor Bob Schnabel Stephanie McKay
Alberta Steve Moore
USMARC – Clay Center Tim Smith Mark Allan
USDA/NRI/CSREES 2006-35616-16697 2006-35205-16888 2006-35205-16701
USDA/ARS 1265-31000-081D 1265-31000-090D 5438-31000-073D
Merial Stewart Bauck
NAAB Godon Doak ABS Global Accelerated Genetics Alta Genetics CRI/Genex Select Sires Semex Alliance Taurus Service
iBMAC Consortium Funding Agencies
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (11) Cole
Use of HD
Currently only 50K subset of SNP used Some increase in accuracy from better
tracking of QTL possible Potential for across breed evaluations Requires few new HD genotypes once
adequate base for imputation developed
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (12) Cole
LD chip
6909 SNP mostly from SNP50 chip 9 Y Chr SNP included for sex validation 13 Mitochondrial DNA SNP Evenly spaced across 30 Chr (increased
density at ends)
Developed to address performance issues with 3K while continuing to provide low cost genotyping
Provides over 98% accuracy imputing 50K genotypes
Included beginning with Nov genomic evaluation
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (13) Cole
Development of LD chip
Consortium included researchers from USA, AUS and FRA
Objective: good imputation performance in dairy breeds
Uniform distribution except heavier at chromosome ends
High MAF, avg MAF over 30% for most breeds
Adequate overlap with 3K
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (14) Cole
Genomic evaluation program steps
Identify animals to genotype
Sample to lab
Genotype sample
Genotype to USDA
Calculate genomic evaluation
Release monthly
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (15) Cole
Responsibilities of requester
Insure animal is properly identified eg HOCANF000123456789
Enroll animal with breed association or insure pedigree on animal and dam reaches AIPL
Collect clean, clearly labeled DNA sample
Get sample to lab in time to be included in desired month’s results
Resolve parentage conflicts quickly
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (16) Cole
Steps to prepare genotypes
Nominate animal for genotyping Collect blood, hair, semen, nasal swab, or
ear punch Blood may not be suitable for twins
Extract DNA at laboratory Prepare DNA and apply to BeadChip Do amplification and hybridization, 3-day
process Read red/green intensities from chip and call
genotypes from clusters
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (17) Cole
What can go wrong
Sample does not provide adequate DNA quality or quantity
Genotype has many SNP that can not be determined (90% call rate required)
Parent-progeny conflicts Pedigree error Sample ID error (Switched samples) Laboratory error Parent-progeny relationship detected that
is not in pedigree
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (18) Cole
Lab QC
Each SNP evaluated for Call Rate Portion Heterozygous Parent-progeny conflicts
Clustering investigated if SNP exceeds limits Number of failing SNP is indicator of
genotype quality Target fewer than 10 SNP in each category
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (19) Cole
Before clustering adjustment
86%
call rate
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (20) Cole
After clustering adjustment
100%
call rate
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (21) Cole
Parentage validation and discovery Parent-progeny conflicts detected
Animal checked against all other genotypes Reported to breeds and requesters Correct sire usually detected
Maternal Grandsire checking SNP at a time checking Haplotype checking more accurate
Breeds moving to accept SNP in place of microsatellites
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (22) Cole
Checking facility Labs place genotype files on AIPL server
Genotypes run through analysis procedures, but not added to database
Reports on missing nominations and QC data returned to Lab
Lab can Detect sample misidentification Improve clustering Apply the same checks used by AIPL
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Imputation Based on splitting the genotype into
individual chromosomes (maternal & paternal contributions)
Missing SNP assigned by tracking inheritance from ancestors and descendents
Imputed dams increase predictor population
3K, LD, & 50K genotypes merged by imputing SNP not on LD or 3K
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (24) Cole
Recessive defect discovery
Check for homozygous haplotypes Most haplotype blocks ~5Mbp long 7 – 90 expected, but 0 observed 5 of top 11 haplotypes confirmed as lethal Investigation of 936 – 52,449 carrier sire
carrier MGS fertility records found 3.0 – 3.7% lower conception rates
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (25) Cole
Breed
BTA chromo-
someLocation, Mbases
Carrier frequency, %
Holstein 5 62–68 4.5 1 93–98 4.6
8 92–97 4.7
Jersey 15 11–16 23.4
Brown Swiss 7 42–47 14.0
Haplotypes impacting fertility
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Collaboration
Full sharing of genotypes with Canada CDN calculates genomic evaluations on
Canadian base Trading of Brown Swiss genotypes with
Switzerland, Germany, and Austria Interbull may facilitate sharing
Agreements with Italy and Great Britain provide genotypes for Holstein Negotiations underway with other
countries
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (27) Cole
Calculation of genomic evaluations
Deregressed values derived from traditional evaluations of predictor animals
Allele substitutions random effects estimated for 45,187 SNP
Polygenic effect estimated for genetic variation not captured by SNP
Selection Index combination of genomic and traditional not included in genomic
Applied to yield, fitness, calving and type traits
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (28) Cole
Reliabilities for young Holsteins*
*Animals with no traditional PTA in April 2011
0100020003000400050006000700080009000
40 45 50 55 60 65 70 75 80
Reliability for PTA protein (%)
Num
ber o
f ani
mal
s 3K genotypes50K genotypes
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (29) Cole
Use of genomic evaluations
Determine which young bulls to bring into AI service
Use to select mating sires
Pick bull dams
Market semen from 2-year-old bulls
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (30) Cole
Use of LD genomic evaluations
Sort heifers for breeding Flush Sexed semen Beef bull
Confirm parentage to avoid inbreeding Predict inbreeding depression better Precision mating considering genomics
(future)
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (31) Cole
Ways to increase accuracy
Automatic addition of traditional evaluations of genotyped bulls when reach 5 years of age
Possible genotyping of 10,000 bulls with semen in repository
Collaboration with more countries Use of more SNP from HD chips Full sequencing – Identify causative
mutations
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (32) Cole
Application to more traits
Animal’s genotype is good for all traits
Traditional evaluations required for accurate estimates of SNP effects
Traditional evaluations not currently available for heat tolerance or feed efficiency
Research populations could provide data for traits that are expensive to measure
Will resulting evaluations work in target population?
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (33) Cole
Impact on producers
Young-bull evaluations with accuracy of early 1st crop evaluations
AI organizations marketing genomically evaluated 2-year-olds
Genotype usually required for cow to be bull dam
Rate of genetic improvement likely to increase by up to 50%
Studs reducing progeny-test programs
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (34) Cole
Summary
Extraordinarily rapid implementation of genomic evaluations
Chips provide genotypes of high accuracy
Comprehensive checking insures quality of genotypes stored
Young-bull acquisition and marketing now based on genomic evaluations
Genotyping of many females because of lower cost low density chips
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (35) Cole
Why genomics works in dairy
Extensive historical data available Well-developed genetic evaluation program Widespread use of AI sires Progeny test programs High valued animals, worth the cost of
genotyping Long generation interval which can be
reduced substantially by genomics
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (36) Cole
History of genomic evaluations
Dec. 2007 BovineSNP50 BeadChip available Apr. 2008 First unofficial evaluation
released Jan. 2009 Genomic evaluations official for
Holstein and Jersey Aug. 2009 Official for Brown Swiss Sept. 2010 Unofficial evaluations from 3K
chipreleased
Dec. 2010 3K genomic evaluations to be official
Sept. 2011 Infinium BovineLD BeadChip available
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (37) Cole
Current sources of data
AIPL CDCB
NAABPDCA
DHI
UniversitiesAIPL Animal Improvement Programs Lab., USDA
CDCBCouncil on Dairy Cattle BreedingDHI Dairy Herd Improvement (milk recording organizations)NAAB National Association of Animal Breeders (AI)PDCAPurebred Dairy Cattle Association (breed registries)
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (38) Cole
Sources of genomic data
Genomic Evaluation Lab
Requester(Ex: AI, breeds)
Dairyproducers
DNAlaboratories
samples
samples
samples
genotypes
nominationsevaluations
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (39) Cole
How does genetic selection work?
ΔG = genetic gain each year reliability = how certain we are about our
estimate of an animal’s genetic merit (genomics can )
selection intensity = how “picky” we are when making mating decisions (management can )
genetic variance = variation in the population due to genetics (we can’t really change this)
generation interval = time between generations (genomics can )
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (40) Cole
Calculation of genomic evaluations
Deregressed values derived from traditional evaluations of predictor animals
Allele substitutions random effects estimated for 45,187 SNP
Polygenic effect estimated for genetic variation not captured by SNP
Selection Index combination of genomic and traditional not included in genomic
Applied to yield, fitness, calving, and type traits
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (41) Cole
Genetic merit of Jersey bulls
2006 2007 2008 2009 20100
100
200
300
400
500
600 Active Genotyped
Breeding Year
Net
Mer
it (
$)
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (42) Cole
What is a SNP genotype worth?
For the protein yield (h2=0.30), the SNP genotype provides information equivalent to an additional 34 daughters
Pedigree is equivalent to information on about 7 daughters
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (43) Cole
And for daughter pregnancy rate (h2=0.04), SNP = 131 daughters
What is a SNP genotype worth?
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (44) Cole
Holstein prediction accuracy
Traita Biasb b REL (%)REL gain
(%)Milk (kg) −64.3 0.92 67.1 28.6Fat (kg) −2.7 0.91 69.8 31.3Protein (kg) 0.7 0.85 61.5 23.0Fat (%) 0.0 1.00 86.5 48.0Protein (%) 0.0 0.90 79.0 40.4PL (months) −1.8 0.98 53.0 21.8SCS 0.0 0.88 61.2 27.0DPR (%) 0.0 0.92 51.2 21.7Sire CE 0.8 0.73 31.0 10.4Daughter CE −1.1 0.81 38.4 19.9Sire SB 1.5 0.92 21.8 3.7Daughter SB − 0.2 0.83 30.3 13.2
a PL=productive life, CE = calving ease and SB = stillbirth.b 2011 deregressed value – 2007 genomic evaluation.
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (45) Cole
Many chips are available
BovineSNP50 Version 1 54,001 SNP Version 2 54,609 SNP 45,187 used in evaluations
HD 777,962 SNP Only 50K SNP used, >1700 in database
LD 6,909 SNP Replaced 3K
HD
50KV2
LD
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (46) Cole
Genotypes and haplotypes
Genotypes indicate how many copies of each allele were inherited
Haplotypes indicate which alleles are on which chromosome
Observed genotypes partitioned into the two unknown haplotypes Pedigree haplotyping uses relatives Population haplotyping finds matching
allele patterns
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (47) Cole
O-Style Haplotypes Chromosome 15
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (48) Cole
Haplotyping program – findhap.f90
Begin with population haplotyping Divide chromosomes into
segments, ~250 to 75 SNP / segment
List haplotypes by genotype match
Similar to fastPhase, IMPUTE End with pedigree haplotyping
Detect crossover, fix noninheritance
Impute nongenotyped ancestors
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (49) Cole
Recessive defect discovery Check for homozygous haplotypes
7 to 90 expected but none observed
5 of top 11 are potentially lethal 936 to 52,449 carrier sire-by-
carrier MGS fertility records 3.1% to 3.7% lower conception
rates Some slightly higher stillbirth
rates Confirmed Brachyspina same way
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (50) Cole
We’re working on new tools
Cole, J.B., and Null, D.J. 2012. AIPL Research Report GENOMIC2: Use of chromosomal predicted transmitting abilities. Available: http://aipl.arsusda.gov/reference/chromosomal_pta_query.html.
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (51) Cole
Impact on producers
Young-bull evaluations with accuracy of early 1st crop evaluations
AI organizations marketing genomically evaluated 2-year-olds
Genotype usually required for cow to be bull dam
Rate of genetic improvement likely to increase by up to 50%
Studs reducing progeny-test programs
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (52) Cole
Expected value of Mendelian sampling no longer equal to 0
Key assumption of animal models References:
Patry, Ducrocq 2011 GSE 43:30 Vitezica et al 2011 Genet Res
(Camb) pp. 1–10.
Bias from Pre-Selection
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (53) Cole
Bulls born in 2008, progeny tested in 2009, with daughter records in 2012, were pre-selected: 3,434 genotyped vs. 1,096
sampled Now >10 genotyped per 1
marketed Potential for bias:
178 genotyped progeny 32 sons progeny tested
Pre-Selection Bias Now Beginning
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (54) Cole
1-Step to incorporate genotypes Flexible models, many recent
studies Foreign data not yet included
Multi-step GEBV, then insert in AM Same trait (Ducrocq and Liu,
2009) Or correlated trait (Mantysaari
and Stranden, 2010; Stoop et al, 2011)
Foreign genotyped bulls included
Methods to Reduce Bias
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (55) Cole
Gene set enrichment analysis-SNP
Gene pathways (G)GWAS results
Score increase is proportional to SNP test statistic
Nominal p-value corrected for multiple testing
Pathways with moderate effects
Holden et al., 2008 (Bioinformatics 89:1669-1683. doi:10.2527/jas.2010-3681)
SNP ranked by significance (L)
SNP in pathway genes (S)
Score increases for each Li in S
Permutation test and FDR
Includes all SNP, S, that are included in L
The more SNP in S that appear near the top of
L, the higher the Enrichment Score
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (56) Cole
Adaptive weight matrix
Need to add this
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (57) Cole
We hope to identify regulatory networks
Fortes et al., 2011 (J. Animal Sci. 89:1669-1683. doi:10.2527/jas.2010-3681)
Candidate genes and pathways that affect age at puberty common to both breeds
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (58) Cole
Network analysis
Fortes et al., 2011 (J. Animal Sci. 89:1669-1683. doi:10.2527/jas.2010-3681)
Gene network – thered center identifieshighly connected nodes.
Subnetwork of interactingtranscription factors fromthe puberty network.
Subnetwork of interactingtranscription factors from a collection of mouse and humandata. (Validation step.)
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (59) Cole
Enriched pathways
Fortes et al., 2011 (J. Animal Sci. 89:1669-1683. doi:10.2527/jas.2010-3681)
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (60) Cole
Transcription factor network
Fortes et al., 2011 (J. Animal Sci. 89:1669-1683. doi:10.2527/jas.2010-3681)
Yellow genes were submitted to database.
Other nodes were mined from FunCoup.
Red: protein-protein interaction
Blue: mRNA coexpression
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (61) Cole
GWAS for birth weight PTA
h
Cole et al.(2013), unpublished data
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (62) Cole
KEGG pathways for birth weight
Waiting on DMB
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (63) Cole
We have divergent populations
0
10
20
30
40
50
60
70
80
1 2 3 4 5 6 7 8 9 10 11 12 >12%DBH
Per
cent
of S
core
s
Cole et al., 2005 (J. Dairy Sci. 88(4):1529–1539)
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (64) Cole
What can we learn from this?
We are not going to find big QTL We may identify gene networks
affecting complex phenotypes We’re going to learn how much
we don’t know about functional genomics in the cow
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Conclusions
…
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (66) Cole
Acknowledgments
…
Keygene N.V., Wageningen, The Netherlands, 29 May 2013 (67) Cole
Questions?
http://gigaom.com/2012/05/31/t-mobile-pits-its-math-against-verizons-the-loser-common-sense/shutterstock_76826245/